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diff --git a/utilities/Alpha_complex/alpha_complex_3d_persistence.cpp b/utilities/Alpha_complex/alpha_complex_3d_persistence.cpp
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-/* This file is part of the Gudhi Library. The Gudhi library
- * (Geometric Understanding in Higher Dimensions) is a generic C++
- * library for computational topology.
- *
- * Author(s): Vincent Rouvreau
- *
- * Copyright (C) 2014 Inria
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <boost/version.hpp>
-#include <boost/program_options.hpp>
-#include <boost/variant.hpp>
-
-#if BOOST_VERSION >= 105400
-#include <boost/container/static_vector.hpp>
-#endif
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Points_3D_off_io.h>
-
-#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/Delaunay_triangulation_3.h>
-#include <CGAL/Alpha_shape_3.h>
-#include <CGAL/Alpha_shape_cell_base_3.h>
-#include <CGAL/Alpha_shape_vertex_base_3.h>
-#include <CGAL/iterator.h>
-
-#include <fstream>
-#include <cmath>
-#include <string>
-#include <tuple>
-#include <map>
-#include <utility>
-#include <vector>
-#include <cstdlib>
-
-#include "alpha_complex_3d_helper.h"
-
-// Alpha_shape_3 templates type definitions
-using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
-using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel>;
-using Fb = CGAL::Alpha_shape_cell_base_3<Kernel>;
-using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
-using Triangulation_3 = CGAL::Delaunay_triangulation_3<Kernel, Tds>;
-using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
-
-// From file type definition
-using Point_3 = Kernel::Point_3;
-
-// filtration with alpha values needed type definition
-using Alpha_value_type = Alpha_shape_3::FT;
-using Object = CGAL::Object;
-using Dispatch =
- CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>,
- CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >,
- std::back_insert_iterator<std::vector<Alpha_value_type> > > >;
-using Cell_handle = Alpha_shape_3::Cell_handle;
-using Facet = Alpha_shape_3::Facet;
-using Edge_3 = Alpha_shape_3::Edge;
-using Vertex_handle = Alpha_shape_3::Vertex_handle;
-
-#if BOOST_VERSION >= 105400
-using Vertex_list = boost::container::static_vector<Alpha_shape_3::Vertex_handle, 4>;
-#else
-using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;
-#endif
-
-// gudhi type definition
-using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Filtration_value = ST::Filtration_value;
-using Simplex_tree_vertex = ST::Vertex_handle;
-using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
-using Persistent_cohomology =
- Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
-
-void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag,
- int &coeff_field_characteristic, Filtration_value &min_persistence);
-
-int main(int argc, char **argv) {
- std::string off_file_points;
- std::string output_file_diag;
- int coeff_field_characteristic;
- Filtration_value min_persistence;
-
- program_options(argc, argv, off_file_points, output_file_diag, coeff_field_characteristic, min_persistence);
-
- // Read the OFF file (input file name given as parameter) and triangulate points
- Gudhi::Points_3D_off_reader<Point_3> off_reader(off_file_points);
- // Check the read operation was correct
- if (!off_reader.is_valid()) {
- std::cerr << "Unable to read file " << off_file_points << std::endl;
- exit(-1);
- }
-
- // Retrieve the points
- std::vector<Point_3> lp = off_reader.get_point_cloud();
-
- // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
- Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
-#ifdef DEBUG_TRACES
- std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
-#endif // DEBUG_TRACES
-
- // filtration with alpha values from alpha shape
- std::vector<Object> the_objects;
- std::vector<Alpha_value_type> the_alpha_values;
-
- Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
- std::back_inserter(the_alpha_values));
-
- as.filtration_with_alpha_values(disp);
-#ifdef DEBUG_TRACES
- std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
-#endif // DEBUG_TRACES
-
- Alpha_shape_3::size_type count_vertices = 0;
- Alpha_shape_3::size_type count_edges = 0;
- Alpha_shape_3::size_type count_facets = 0;
- Alpha_shape_3::size_type count_cells = 0;
-
- // Loop on objects vector
- Vertex_list vertex_list;
- ST simplex_tree;
- Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
- std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
- for (auto object_iterator : the_objects) {
- // Retrieve Alpha shape vertex list from object
- if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
- vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
- count_cells++;
- } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
- vertex_list = from_facet<Vertex_list, Facet>(*facet);
- count_facets++;
- } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
- vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
- count_edges++;
- } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
- count_vertices++;
- vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
- }
- // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
- Simplex_tree_vector_vertex the_simplex;
- for (auto the_alpha_shape_vertex : vertex_list) {
- Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
- if (the_map_iterator == map_cgal_simplex_tree.end()) {
- // alpha shape not found
- Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
-#ifdef DEBUG_TRACES
- std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
-#endif // DEBUG_TRACES
- the_simplex.push_back(vertex);
- map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
- } else {
- // alpha shape found
- Simplex_tree_vertex vertex = the_map_iterator->second;
-#ifdef DEBUG_TRACES
- std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
-#endif // DEBUG_TRACES
- the_simplex.push_back(vertex);
- }
- }
- // Construction of the simplex_tree
- Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator);
-#ifdef DEBUG_TRACES
- std::cout << "filtration = " << filtr << std::endl;
-#endif // DEBUG_TRACES
- simplex_tree.insert_simplex(the_simplex, filtr);
- GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values");
- ++the_alpha_value_iterator;
- }
-
-#ifdef DEBUG_TRACES
- std::cout << "vertices \t\t" << count_vertices << std::endl;
- std::cout << "edges \t\t" << count_edges << std::endl;
- std::cout << "facets \t\t" << count_facets << std::endl;
- std::cout << "cells \t\t" << count_cells << std::endl;
-
- std::cout << "Information of the Simplex Tree: " << std::endl;
- std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " ";
- std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
- std::cout << " Dimension = " << simplex_tree.dimension() << " ";
-#endif // DEBUG_TRACES
-
-#ifdef DEBUG_TRACES
- std::cout << "Iterator on vertices: " << std::endl;
- for (auto vertex : simplex_tree.complex_vertex_range()) {
- std::cout << vertex << " ";
- }
-#endif // DEBUG_TRACES
-
- // Sort the simplices in the order of the filtration
- simplex_tree.initialize_filtration();
-
- std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
- // Compute the persistence diagram of the complex
- Persistent_cohomology pcoh(simplex_tree, true);
- // initializes the coefficient field for homology
- pcoh.init_coefficients(coeff_field_characteristic);
-
- pcoh.compute_persistent_cohomology(min_persistence);
-
- // Output the diagram in filediag
- if (output_file_diag.empty()) {
- pcoh.output_diagram();
- } else {
- std::cout << "Result in file: " << output_file_diag << std::endl;
- std::ofstream out(output_file_diag);
- pcoh.output_diagram(out);
- out.close();
- }
-
- return 0;
-}
-
-void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag,
- int &coeff_field_characteristic, Filtration_value &min_persistence) {
- namespace po = boost::program_options;
- po::options_description hidden("Hidden options");
- hidden.add_options()("input-file", po::value<std::string>(&off_file_points),
- "Name of file containing a point set. Format is one point per line: X1 ... Xd ");
-
- po::options_description visible("Allowed options", 100);
- visible.add_options()("help,h", "produce help message")(
- "output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
- "Name of file in which the persistence diagram is written. Default print in std::cout")(
- "field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11),
- "Characteristic p of the coefficient field Z/pZ for computing homology.")(
- "min-persistence,m", po::value<Filtration_value>(&min_persistence),
- "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
- "intervals");
-
- po::positional_options_description pos;
- pos.add("input-file", 1);
-
- po::options_description all;
- all.add(visible).add(hidden);
-
- po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm);
- po::notify(vm);
-
- if (vm.count("help") || !vm.count("input-file")) {
- std::cout << std::endl;
- std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
- std::cout << "of a 3D Alpha complex defined on a set of input points.\n \n";
- std::cout << "The output diagram contains one bar per line, written with the convention: \n";
- std::cout << " p dim b d \n";
- std::cout << "where dim is the dimension of the homological feature,\n";
- std::cout << "b and d are respectively the birth and death of the feature and \n";
- std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
- std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
- std::cout << visible << std::endl;
- exit(-1);
- }
-}
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